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15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”

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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Neurogenomics".

Deadline for manuscript submissions: closed (25 November 2025) | Viewed by 11641

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Dr. Claudia Ricci

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Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
Interests: neurogenetics; motor neuron diseases; amyotrophic lateral sclerosis; genotype-phenotype correlations; gene variant consequences; microRNAs
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Prof. Dr. Micheal Palladino

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Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
Interests: metabolism; glycolysis; mitochondira; genetics; genetic models; biochemistry; therapy development; neuromuscular function and neurogenetics
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Special Issue Information

Dear Colleagues,

This Special Issue, titled '15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”', will bring together high-quality research articles, reviews, communications, and perspectives exploring the interplay between genomics and nervous system function, development, and diseases. The Special Issue celebrates the 15th anniversary of Genes, as well as the 10th anniversary of the journal receiving its first impact factor. This Issue will focus on recent advances in genomics and genetics research related to the diagnosis, treatment, and prognosis of neurological disorders, as well as neurodevelopment and pathogenic mechanisms. We encourage the Editorial Board Members of the 'Neurogenomics' section to contribute feature papers reflecting the latest progress in their field of research, or to invite relevant senior experts and colleagues to contribute to this Special Issue. Our aim is to showcase our section as an attractive open access publishing platform for neurogenomics research.

Possible topics include, but are not limited to, the following:

Multi-omics studies on neurological function and development.
Functional genomics approaches in neurological diseases.
Genetics of neurological monogenic diseases and complex disorders.
Genetic testing and molecular diagnostics of neurological diseases.
Genotype–phenotype correlations.
Precision medicine.
Pharmacogenetics and pharmacogenomics.
Advanced therapies (gene therapy/ targeted genome editing/genetically engineered cell therapy/RNA- and small nucleic acid-based therapeutics) for neurological diseases.

Dr. Claudia Ricci
Prof. Dr. Micheal Palladino
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

genomics
neurological diseases
multi-omics studies
brain development and function
precision medicine
pathogenic mechanisms

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Published Papers (10 papers)

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16 pages, 1988 KB

Open AccessArticle

Clinical Insights into the Neurodevelopmental Impact of 16p CNVs in an Italian Clinical Cohort

by Ilaria La Monica, Maria Rosaria Di Iorio, Antonia Sica, Lucio Pastore and Barbara Lombardo

Genes 2026, 17(2), 247; https://doi.org/10.3390/genes17020247 - 21 Feb 2026

Viewed by 814

Abstract

Background: Neurodevelopmental disorders (NDDs) are a heterogeneous group of conditions characterized by cognitive, behavioral, and developmental impairments, frequently linked to structural genomic alterations. Copy number variants (CNVs) involving chromosome 16, particularly the short arm 16p, are recognized contributors to neurodevelopmental variability. Despite increasing international evidence, data from Italian clinical cohorts are still limited. Methods: We investigated 1200 patients referred for genetic evaluation due to suspected NDDs, including autism spectrum disorder (ASD), intellectual disability (ID), global developmental delay, and language impairment. All individuals underwent array comparative genomic hybridization (a-CGH) analysis, and identified variants were correlated with detailed clinical, cognitive, and behavioral assessments. The analysis focused on recurrent CNVs at 16p11.2, 16p13.3, and 16p13.11, regions containing dosage-sensitive genes relevant to neurodevelopment. Results: CNVs involving the 16p region were identified in 96 patients (8% of the cohort), encompassing both deletions and duplications. Deletions were mainly associated with developmental delay, language deficits, and ASD-related features, whereas duplications were more frequently linked to behavioral dysregulation, attentional deficits, and variable cognitive impairment. Marked phenotypic variability was observed among individuals carrying similar CNVs, suggesting the contribution of modifying genetic or environmental factors. In a subset of patients, additional CNVs were identified, potentially exacerbating clinical severity, consistent with the two-hit model. Conclusions: This study confirms a strong association between recurrent 16p CNVs and a wide spectrum of neurodevelopmental phenotypes in an Italian clinical cohort. The findings emphasize the diagnostic utility of systematic genomic screening and the importance of an integrated genotype–phenotype approach to improve clinical interpretation, management, and genetic counseling in NDDs. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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17 pages, 1952 KB

Open AccessArticle

ABCC6 Heterozygosity as Genetic Predisposition to Cerebrovascular Disease Across Ages

by Giulia Amico, Mariasavina Severino, Marta Bertamino, Rosario Pascarella, Domenico Tortora, Sara Signa, Marta Rusmini, Andrea Rossi, Isabella Ceccherini and Marialuisa Zedde

Genes 2026, 17(2), 226; https://doi.org/10.3390/genes17020226 - 11 Feb 2026

Viewed by 646

Abstract

Background: Heterozygosity for pathogenic variants in the ABCC6 gene has been associated with an increased incidence of cerebrovascular diseases. This study aims to characterize the prevalence and clinical and neuroradiological phenotypes associated with monoallelic and biallelic ABCC6 variants in pediatric and adult patients presenting with arterial ischemic stroke or cerebral small vessel disease (CSVD). Methods: We conducted a retrospective observational study on 143 consecutive patients (48 pediatric, 24 juvenile, 71 adult) diagnosed with ischemic stroke or CSVD of unknown etiology. Clinical and neuroradiological data were collected and analyzed in relation to the identified genetic variants through next-generation sequencing. Results: Among the patients, 16 (11.2%) tested positive for causative variants in the ABCC6 gene, with 11 subjects carrying monoallelic variants and 5 carrying biallelic variants. Patients with biallelic variants exhibited severe and complex vasculopathy, with a high incidence of early ischemic events. In contrast, monoallelic carriers predominantly presented with microvascular disease manifestations, including lacunar strokes and signs of CSVD. Conclusions: The results suggest a significant age-dependent phenotypic divergence in patients with ABCC6 variants, highlighting the impact of heterozygosity on cerebrovascular health. Identifying these variants may enhance risk stratification and inform management strategies in patients with traditional vascular risk factors. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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20 pages, 3030 KB

Open AccessArticle

Behavioral Features in Phelan–McDermid Syndrome: Characteristics and Genetic and Metabolic Contributions in a Cohort of 56 Individuals

by Emily Payne, Bridgette A. Moffitt, Lindsay M. Oberman, Laura Beamer, Sujata Srikanth, Lauren Nicole Cascio, Kelly Jones, Lavanya Jain, Rini Pauly, Melanie May, Cindy Skinner, Carrie Buchanan, Barbara G. DuPont, Rebekah R. Martin, R. Curtis Rogers, Katy Phelan, Sara M. Sarasua, Walter E. Kaufmann and Luigi Boccuto

Genes 2026, 17(2), 202; https://doi.org/10.3390/genes17020202 - 8 Feb 2026

Viewed by 793

Abstract

Background/Objectives: Phelan–McDermid syndrome (PMS), caused by either chromosome 22q13.3 deletions or pathogenic/likely pathogenic variants in the SHANK3 gene, is a rare neurodevelopmental disorder. Behavioral issues greatly impair the quality of life for affected individuals and their families. This genotype–phenotype study intended to further characterize key behavioral features and their genetic and metabolic correlates in PMS. Methods: We conducted a cross-sectional analysis of data on 56 individuals with PMS. Autistic and related behaviors were assessed with the Autism Diagnosis Interview—Revised (ADI-R) and adaptive behavior skills were assessed with the Vineland Adaptive Behavior Scales-Third Edition (Vineland-3), both covering multiple aspects of communication, socialization and abnormal behaviors. Genetic diagnostic information on deletions or pathogenic variants was supplemented with the sequencing data of nine candidate genes on 22q13.3. Metabolic data were obtained using the Biolog Phenotype Mammalian MicroArray plates (PM-M). Results. Every subject in the cohort presented either prominent autistic behavior or adaptive behavior impairment, 55.4% of them meeting the ASD cutoff in every ADI-R domain and 92.9% scoring in the lowest level of adaptive behavior (range of 20–70). Individuals with SHANK3 variants had lower adaptive behavioral skills than those with 22q13 deletions regardless of deletion size, while genomic parameters were largely unrelated to ADI-R scores. Metabolic profiling identified unique profiles of individuals with PMS compared with controls, while distinct profiles distinguished those who met or did not meet the ADI-R ASD cutoff. Cluster analyses revealed groups of individuals with ASD and other clinical features. Conclusion. This study highlighted the importance of SHANK3 in adaptive behavioral skills and uncovered potential metabolic biomarkers of therapeutic relevance. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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14 pages, 4301 KB

Open AccessArticle

Transcriptome- and Epigenome-Wide Association Studies of Tic Spectrum Disorder in Discordant Monozygotic Twins

by Jonas Dalsberg, Cathrine Jespersgaard, Amanda M. Levy, Anna Maria Asplund, Frederik Otzen Bagger, Nanette M. Debes, Qihua Tan, Zeynep Tümer and Mathis Hildonen

Genes 2026, 17(1), 97; https://doi.org/10.3390/genes17010097 - 18 Jan 2026

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Abstract

Background: Tic spectrum disorder (TSD), encompassing Tourette syndrome and chronic tic disorder, is a childhood-onset neurodevelopmental condition with complex genetic and environmental contributions. Heritable components have been implicated in TSD, but no clear genetic mechanisms have been identified. Significant aspects of TSD etiology remain unclear, with key uncertainties concerning the role of environmental influences in its development. In this study, we aimed to identify environmentally induced epigenomic and transcriptomic changes contributing to TSD pathology by investigating genetically similar monozygotic twins discordant for TSD. Methods: To investigate environmentally driven mechanisms, we analyzed peripheral blood from eleven monozygotic twin pairs, either discordant or concordant for TSD, using RNA sequencing and DNA methylation analysis. Results: Differential expression analysis identified a dozen differentially expressed genes between TSD and non-TSD individuals, most of which were long non-coding RNAs or pseudogenes. Expression of the small RNA gene RNY1 was significantly associated with tic severity, suggesting involvement of immune-related processes. DNA methylation (DNAm) analysis revealed ~30,000 probes with a nominal p < 0.05, however none of these were significant after multiple testing correction. Expression quantitative trait methylation (eQTM) analysis identified 236 methylation-associated genes. Gene set enrichment analysis demonstrated broad downregulation in TSD individuals for pathways related to translation, RNA processing, and neurobiological functions, with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including ribosome, nucleocytoplasmic transport, pluripotency signaling, and nicotine addiction. Conclusions: These results suggest that environmentally influenced gene expression may contribute to TSD pathogenesis through dysregulation of immune and neuronal pathways. Despite a small sample size, the monozygotic twin design provides strong control for genetic background and identifies significant differences that contribute to the understanding of the underlying molecular mechanisms of TSD. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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18 pages, 531 KB

Open AccessArticle

Somatostatin-Expressing Neurons Regulate Sleep Deprivation and Recovery

by Kenta Kobayashi and Y-h. Taguchi

Genes 2026, 17(1), 51; https://doi.org/10.3390/genes17010051 - 1 Jan 2026

Viewed by 1222

Abstract

Background/Objectives We re-analyzed publicly available gene expression profiles from the male mouse cortex under conditions of sleep deprivation (SD) using tensor decomposition-based unsupervised feature extraction, originally proposed by one of the authors in 2017. Methods We focused on two distinct expression patterns: genes whose levels were altered in SD and failed to normalize during recovery sleep (RS), and genes that overshot normal levels during RS. This selection excluded the expected “altered in SD and recovered in RS” pattern, which was not significantly observed. These two gene sets showed substantial overlap but were still distinct from each other. Results The analysis revealed that the selected gene sets were enriched in various brain regions as evidenced through clustering in the Allen Brain Atlas. This suggests that the successful selection identified biologically meaningful genes. Furthermore, somatostatin (Sst)-expressing neuronal clusters were among the most highly enriched. Conclusions Given that sst is already implicated in SD and RS, our fully data-driven transcriptomic analysis successfully identified the activity of sst during SD and RS. These findings reveal that Sst-expressing neurons may play a key role in SD. These results were further validated using AlphaGenome by uploading the selected genes to it. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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24 pages, 27293 KB

Open AccessArticle

Canine Neuronal Ceroid Lipofuscinosis-like Disorder Associated with Sequence Variants in AP3B1 and TRAPPC9

by Alexander Then, Rebecca Welly, Garrett Bullock, Lucie Chevallier and Martin L. Katz

Genes 2025, 16(11), 1370; https://doi.org/10.3390/genes16111370 - 11 Nov 2025

Cited by 1 | Viewed by 1491

Abstract

Background/Objectives: A Petit Bleu de Gascogne (PBDG) dog presented with a progressive neurological disorder characterized by hind-limb weakness, anxiety and hallucinatory episodes, lip smacking, progressive vision loss, muscle atrophy, and ataxia. Magnetic resonance imaging revealed diffuse brain atrophy. The dog was euthanized at approximately 23 months of age due to the progression of neurological signs. A study was undertaken to identify the molecular genetic basis of the disorder in this dog. Methods: Microscopic analyses were performed to characterize the disease pathology and whole-genome sequencing was performed to identify the molecular genetic basis of the disorder. Results: The proband exhibited pronounced accumulations of autofluorescent intracellular inclusions in the brain, retina, and heart with ultrastructural appearances similar to those of lysosomal storage bodies that accumulate in the neuronal ceroid lipofuscinosis (NCLs), a group of progressive neurodegenerative disorders. Whole-genome sequence analysis of DNA from the proband identified homozygous missense variants in AP3B1 and TRAPPC9 that encode proteins involved in sorting and transport of proteins through the Golgi apparatus to lysosomes. Screening of unaffected PBDGs for these variants identified dogs that were homozygous for either variant, but no other dogs that were homozygous for both. Conclusions: These findings raise the possibility that the disease involves the combined influence of the two variants, and that the proteins encoded by these genes interact within the Golgi apparatus to mediate protein sorting and transport to lysosomes. An alteration in this interaction could underlie the NCL-like lysosomal storage disorder observed in the proband. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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16 pages, 1338 KB

Open AccessArticle

Newly Identified TPI Deficiency Treatments Function for Novel Disease-Causing Allele, TPI1^R5G

by Joseph R. Figura, Presley Roberts, Riley Sawka, Maci Chambers, Marcelo Claudio, Laura L. Vollmer, Andreas Vogt, Gregg E. Homanics, Eduard van Beers, Mylene Donge, Emmanuel Scalais, Arthur Sorlin, Ariana J. Jou, Andrew P. VanDemark and Michael J. Palladino

Genes 2025, 16(10), 1205; https://doi.org/10.3390/genes16101205 - 14 Oct 2025

Viewed by 1251

Abstract

Background/Objectives: Triosephosphate Isomerase (TPI) is a glycolytic enzyme known to be associated with TPI deficiency, a severe form of childhood-onset glycolytic enzymopathy associated with hemolytic anemia, neuromuscular impairment and early death. Most often the disease results from the common TPI1^E105D mutation, which can be either homozygous or compound heterozygous with another allele. Methods: We purified TPI^R5G protein, studied mutant protein biochemistry, established and characterized TPI^R5G/f.s.patient cells, and investigated newly identified compounds for their efficacy in vitro using Western blot and TPI activity assays. Results: We identified novel TPI1 alleles that result in TPI Deficiency with an atypical presentation lacking anemia and with more slowly developing neurologic and locomotor impairment. The patient was found to be compound heterozygous with a missense mutation resulting in an R5G amino acid substitution and a frameshift mutation that is a predicted null allele. To better understand disease pathogenesis in this patient, we expressed and purified the TPI^R5G human protein and studied it biochemically in addition to studying TPI^R5G/f.s.patient cells. We discovered that purified TPI^R5G protein has wildtype activity with modestly increased dimer stability. We also discovered that steady-state TPI protein levels were markedly reduced, suggesting that the instability of the mutant protein underlies disease pathogenesis. We tested compounds recently identified in a screen for novel TPI Df therapies for their efficacy in TPI^R5G/f.s.patient cells. All three compounds significantly increased TPI protein levels in patient cells. As expected, since the mutant protein retains essentially wild type activity, the increase in TPI protein levels also resulted in a significant increase in TPI activity. Conclusions: These results establish TPI^R5G as a TPI Df allele, demonstrate that reduced stability of the mutant protein underlies pathogenesis akin to other disease-causing alleles, and suggest that recently discovered developing therapies will likely function broadly and should be developed as potential TPI Df therapies. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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16 pages, 300 KB

Open AccessArticle

Chromosome 12 and Environmental Factors in Parkinson’s Disease: An All of Us Data Analysis

by Kenta Abe and Karen Niemchick

Genes 2025, 16(10), 1197; https://doi.org/10.3390/genes16101197 - 13 Oct 2025

Viewed by 1617

Abstract

Background/Objectives: Parkinson’s disease (PD) is a neurodegenerative disease that develops with age and is related to a decline in motor function. Studies suggest that the causes may be based on genetic dysfunction including PARK gene mutations and environmental factors. Methods: To explore those factors, we used multivariable logistic regression to obtain odds ratios (ORs) and adjusted ORs by using the All of Us Dataset which contains genomic, blood test, and other environmental data. Results: On Chromosome 12, there were 3709 candidate genetic polymorphisms (GPs) that are associated with PD. Of those GPs, fourteen GPs had high ORs which are similar to the OR of the PARK8 gene G2019S mutation. Of those 3709 GPs, a 2.00-fold change in OR was observed in five GPs located at bases 53,711,362 (OR = 4.86, 95% CI [1.46, 16.18]), 31,281,818 (OR = 4.37, 95% CI [1.02, 18.82]), 101,921,705 (OR = 5.38, 95% CI [1.23, 23.51]), 47,968,795 (OR = 7.82, 95% CI [1.81, 33.83]), and 112,791,809 (OR = 8.05, 95% CI [1.85, 35.05]) by calcium, Vitamin D, and alcohol intake and were statistically significant. Conclusions: The results suggest that the progression of some PD caused by certain GPs can be delayed or prevented by the environmental factors above. In February 2025, All of Us released the CT Dataset v.8 which has a 50% increase in the number of participants. Potentially, it may be possible to research more GPs and environmental factors. In future studies, we would like to explore other environmental factors and GPs on other chromosomes. It is believed that specific GPs may tailor current treatments and qualify patients for clinical trials. Additionally, genetic knowledge may help increase accuracy in clinical trials. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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18 pages, 2638 KB

Open AccessArticle

RNA Polymerase I Dysfunction Underlying Craniofacial Syndromes: Integrated Genetic Analysis Reveals Parallels to 22q11.2 Deletion Syndrome

by Spencer Silvey, Scott Lovell and Merlin G. Butler

Genes 2025, 16(9), 1063; https://doi.org/10.3390/genes16091063 - 10 Sep 2025

Viewed by 1448

Abstract

Background/Objective: POLR1A and related gene variants cause craniofacial and developmental syndromes, including Acrofacial Dysostosis-Cincinnati, Treacher-Collins types 2–4, and TWIST1-associated disorders. Using a patient case integrated with molecular analyses, we aimed to clarify shared pathogenic mechanisms and propose these conditions as part of a spectrum of RNA polymerase I (Pol I)–related ribosomopathies. Methods: A patient with a heterozygous POLR1A variant underwent clinical evaluation. Findings were integrated with a literature review of craniofacial syndromes to identify overlapping fea tures. Protein-protein and gene-gene interactions were analyzed with STRING and Pathway Commons, a structural modeling of POLR1A assessed the mutation’s impact. Results: The patient exhibited features overlapping with Sweeney-Cox, Saethre-Cox, Robinow-Sorauf, and Treacher-Collins types 2–4, supporting a shared spectrum. Computational analyses identified POLR1A-associated partners and pathways converging on Pol I function, ribosomal biogenesis, and nucleolar processes. Structural modeling of the Met496Ile variant suggested disruption of DNA binding and polymerase activity, linking molecular dysfunction to the clinical phenotype. Conclusion: Significant clinical and genetic overlap exists among Saethre-Chotzen, Sweeney-Cox, Treacher-Collins types 2–4, and Acrofacial Dysostosis-Cincinnati. POLR1A and related Pol I subunits provide a mechanistic basis through impaired nucleolar organization and rRNA transcription, contributing to abnormal craniofacial development. Integrative protein, gene, and structural analyses support classifying these syndromes as Pol I–related ribosomopathies, with implications for diagnosis, counseling, and future mechanistic or therapeutic studies. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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Review

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26 pages, 506 KB

Open AccessReview

Alzheimer’s 2030: From Precision Genomics to Artificial Intelligence

by Valeria D’Argenio, Rossella Tomaiuolo, Silvia Bargeri and Giulia Sancesario

Genes 2026, 17(2), 233; https://doi.org/10.3390/genes17020233 - 12 Feb 2026

Viewed by 1073

Abstract

Alzheimer’s disease (AD) represents a critical global health challenge, with its prevalence and associated costs expected to double significantly by 2030 and 2050. While lifestyle interventions are crucial, sporadic late-onset AD has a substantial genetic component (40–80% heritability), though known variants limit the scope of traditional precision medicine. Crucially, sex and gender are significant risk determinants, with women accounting for two-thirds of cases due to a complex interplay of biological and sociocultural factors. This review focuses on the influence of genetic and gender-related factors, examining large-scale genome-wide association studies (GWASs) and their role in developing advanced genetic risk scores (GRS) for precision genomics. We also explore the potential of Artificial Intelligence (AI) for multimodal big data analysis and digital health tools to promote personalized prevention and emerging concerns about ethics, privacy and data treatment. The convergence of these findings underscores the urgent need for a genetic-, sex- and gender-informed precision-medicine approach to AD. Full article

(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in “Neurogenetics and Neurogenomics”)

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